X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 100 mM Tris-HCl, pH 8.0, 20-35% PEG3350, 3 mM GDP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.03 α = 90
b = 121.04 β = 90
c = 47.82 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-07-18
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.55 44.48 98.0 -- -- -- -- 16553 16222 2.8 2.8 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.55 2.69 86.8 -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.55 44.48 -- 2.8 15385 15385 814 100.0 -- 0.24296 0.24064 0.28573 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.55 2.617 -- 40 839 0.318 0.383 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.266
Anisotropic B[1][1] 1.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.46
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.001
r_scbond_it 1.881
r_mcangle_it 1.167
r_mcbond_it 0.646
r_gen_planes_refined 0.008
r_chiral_restr 0.105
r_dihedral_angle_4_deg 20.092
r_dihedral_angle_3_deg 18.72
r_dihedral_angle_2_deg 36.889
r_dihedral_angle_1_deg 5.523
r_angle_refined_deg 1.556
r_bond_refined_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3704
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 64

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
Phenix Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
Phenix model building
ADSC version: Quantum data collection